In response to the adverse changes in the navigation channel of the project section during the bridge construction，we analyze the measured hydrology，topography，and channel maintenance before and after construction based on the construction of the main pier’s open caisson of Husutong Yangtze River Highway-Railway Bridge. The results show that caissons sand suction operation and riverbed scour are the direct reasons for the recent waterway siltation and substantial increase of maintenance in the Nantong channel. So，the adverse influence of the construction scheme on the channel shall be considered in advance in the early stage of the pier structure study.